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The Natural Variance Of The Arabidopsis Floral Secondary Metabolome, Takayuki Tohge, Monica Borghi, Alisdair R. Fernie

Biology Faculty Publications

Application of mass spectrometry-based metabolomics enables the detection of genotype-related natural variance in metabolism. Differences in secondary metabolite composition of flowers of 64 Arabidopsis thaliana (Arabidopsis) natural accessions, representing a considerable portion of the natural variation in this species are presented. The raw metabolomic data of the accessions and reference extracts derived from flavonoid knockout mutants have been deposited in the MetaboLights database. Additionally, summary tables of floral secondary metabolite data are presented in this article to enable efficient re-use of the dataset either in metabolomics cross-study comparisons or correlation-based integrative analysis of other metabolomic and phenotypic features such as …

The Relationship Between Site Contamination And Native Plant Success In Butte, Mt: Implications For Future Restoration, Jared Trilling

Graduate Theses & Non-Theses

Interest in ecological restoration of mining impacted areas, as opposed to traditional reclamation practices, has been increasing in recent years. Holistic ecological restoration is preferable to traditional reclamation practices as it provides better ecological function, biodiversity, and human enjoyment. However, legacy effects of mining, such as metals contamination and poor growing substrates, has hampered restoration efforts and further, there is little research on primary succession of these novel ecosystems. There is also scant information on many native plant species responses to contamination.

This study focuses on developing plant-contaminant relationships to guide restoration planting decisions. We look at Butte, MT, an …

Organismal Biology (Georgia Tech), Shana Kerr, David Garton

Biological Sciences Grants Collections

This Grants Collection for Organismal Biology was created under a Round Six ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

Chronic Administration Of Probiotic L. Rhamnosus Increases Anxiety-Like Behavior In Group-Housed Male Long Evans Rats, Parker Maddison Griff

Honors Theses

Early life stress is a risk factor for later development of alcohol use disorders and anxiety disorders in humans. Using rodent experimental models, we know that rats experiencing social isolation as early-life stress exhibit greater anxiety-like behavior and alcohol consumption than rats housed in groups. Examining potential preventive strategies, we investigated the effects of probiotics, which have previously been shown to decrease rodent anxiety-like behavior, on the relationship between early-life stress and anxiety-like behavior in rats. We hypothesized that probiotics consumption would decrease anxiety-like behavior in socially isolated rats, as well as in rats housed in groups. To our surprise, …

Microbial Diversity In The Eukaryotic Sar Clade: Illuminating The Darkness Between Morphology And Molecular Data, Jean David Grattepanche, Laura M. Walker, Brittany M. Ott, Daniela L. Paim Pinto, Charles F. Delwiche, Christopher E. Lane, Laura A. Katz

Biological Sciences: Faculty Publications

Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described species that are missing molecular data. The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for …

Analysis Of A Functional Heterologous Chromosomal Replication Origin Transplant In E. Coli, Rohit Pradip Kadam

Theses and Dissertations

To ensure that all cells replicate their genomes faithfully before they divide, the initiation step of chromosome replication must be tightly regulated during the cell cycle. In bacteria, new rounds of replication are triggered by the assembly of a higher order protein complex, termed the orisome, that unwinds a well-defined origin (oriC) region on the circular chromosome, and prepares it for new replication forks. Orisomes comprise multiple copies of a highly conserved initiator protein, DnaA, and instructions for ordered orisome assembly are encoded into the oriC nucleotide sequence of nearly all bacteria as specifically-spaced clusters of 9 base pair (bp) …

The Geometry Of Nutrient Space–Based Life-History Trade-Offs: Sex-Specific Effects Of Macronutrient Intake On The Trade-Off Between Encapsulation Ability And Reproductive Effort In Decorated Crickets, James Rapkin, Clarissa M. House, John Hunt, Scott K. Sakaluk, Kim Jensen, C. Ruth Archer, Enrique Del Castillo

Faculty Publications – Biological Sciences

Life-history theory assumes that traits compete for limited resources, resulting in trade-offs. The most commonly manipulated resource in empirical studies is the quantity or quality of diet. Recent studies using the geometric framework for nutrition, however, suggest that trade-offs are often regulated by the intake of specific nutrients, but a formal approach to identify and quantify the strength of such trade-offs is lacking. We posit that trade-offs occur whenever life-history traits are maximized in different regions of nutrient space, as evidenced by nonoverlapping 95% confidence regions of the global maximum for each trait and large angles (θ) between linear nutritional …

An Assessment Of Dna Extraction Protocols For Herbarium Specimen: The Case Of Uaeu Herbarium, Mouza Ali Hasan Mohammad Alshehhi

Biology Theses

The herbarium collections have become vastly used due to the recent developments in molecular techniques. Molecular techniques such as DNA extraction and DNA sequencing are playing an important role in studying genetic makeup of plant and identifying the evolutionary relationship using DNA bar coding. Herbarium collection is considered as one of the potential source to access the genetic material of the extinct plant species. Study focused on the DNA isolation process using five isolation techniques: Maxwell, Synergy, Qiagen, I-Genomic , and CTAB on herbarium desert/medicine plant: Inula Helenium, Chenopodium album, Salsola Kali, Haloxylon Persicum, Atriplex Halimus and compared them with …

Artemisia Scoparia Reduces The Effects Of Tnfα-Induced Lipolysis In Murine Adipocytes, Ruth Dunn

Honors Capstones

No abstract provided.

The Evolutionary Significance Of Body Size In Burying Beetles, Ashlee Nichole Momcilovich

Theses and Dissertations

Body size is one of the most commonly studied traits of an organism, which is largely due to its direct correlation with fitness, life history strategy, and physiology of the organism. Patterns of body size distribution are also often studied. The distribution of body size within species is looked at for suggestions of differential mating strategies or niche variation among ontogenetic development. Patterns are also examined among species to determine the effects of competition, environmental factors, and phylogenetic inertia. Finally, the distribution of body size across the geographic range of a species or group of closely related is looked at …

The Role Of Vitamin D Receptors In Gastric Epithelial Homeostasis, Ifrah Ismail Ali

Biology Theses

The gastric epithelium consists of different types of cells, which are involved in gastric homeostasis by balancing cell proliferation and differentiation. This process involves several signaling molecules such as growth factors, hormones and vitamins. Vitamin D3 (VD3) is engaged in several biological activities. It plays a role in cell differentiation, cell proliferation, immune response and also regulates calcium homeostasis. The biological activities of VD3 are mediated by vitamin D receptor (VDR). Target tissues of VD3 in the gastrointestinal tract were identified earlier in intestine, colon and gastric cancer tissues; however, the normal expression of VDR in stomach is poorly studied. …

Effect Of Feeding Frequency And Stocking Density On Tilapia Oreochromis Niloticus And Lettuce Lactuca Sativa Production In Aquaponics System Under The Uae Condition And Business Enterprise Analysis, Ahmed Abdelrahman Mohamed Abdelrahman

Biology Theses

This thesis was carried out to investigate the impact of various Tilapia (Oreochromisniloticus) feeding frequency and stocking density on quality and quantity of organic lettuce that is produced in an aquaponic system, knowing that they affect the nutrient content in water. Business analysis through enterprise budget was developed considering different feeding frequency and stocking density of the fish to predict the business efficiency of the system, and the net incomes were as high as AED 34,394 and AED 46,637, respectively. On the other hand, lettuce was seeded in a culture raceway. The duration of the experiments was decided to be …

Maternal Choline Supplementation During Normal Murine Pregnancy Alters The Placental Epigenome: Results Of An Exploratory Study, Sze Ting (Cecilia) Kwan, Julia H. King, Jennifer K. Grenier, Jian Yan, Xinyin Jiang, Mark S. Roberson, Marie A. Caudill

Publications and Research

The placental epigenome regulates processes that affect placental and fetal development, and could be mediating some of the reported effects of maternal choline supplementation (MCS) on placental vascular development and nutrient delivery. As an extension of work previously conducted in pregnant mice, the current study sought to explore the effects of MCS on various epigenetic markers in the placenta. RNA and DNA were extracted from placentas collected on embryonic day 15.5 from pregnant mice fed a 1X or 4X choline diet, and were subjected to genome-wide sequencing procedures or mass-spectrometry-based assays to examine placental imprinted gene expression, DNA methylation patterns, …

Molecular Phylogenetics Of Floridian Boletes, Arian Farid

USF Tampa Graduate Theses and Dissertations

The boletes are macrofungi which have undergone extensive taxonomic revisions since the advent of molecular tools. To further our understanding of the boletes in peninsular Florida, we sequenced two common Floridian boletes, and analyzed them with molecular phylogenetic tools. Boletus rubricitrinus, a common Florida bolete often found in lawns under Quercus, and likely has a distribution that extends to Texas. Based on ITS and LSU sequences and morphological studies, this species belongs in the genus Pulchroboletus. As the holotype is in poor condition, an epitype is established here. A thorough description of macroscopic and microscopic features is also provided for …

Effect Of Microbes On The Growth And Physiology Of The Dioecious Moss, Ceratodon Purpureus, Caitlin Ann Maraist

Dissertations and Theses

The microorganisms colonizing plants can have a significant effect on host phenotype, mediating such processes as pathogen resistance, stress tolerance, nutrient acquisition, growth, and reproduction. Research regarding plant-microbe interactions has focused almost exclusively on vascular plants, and we know comparatively little about how bryophytes -- including mosses, liverworts, and hornworts -- are influenced by their microbiomes. Ceratodon purpureus is a dioecious, cosmopolitan moss species that exhibits sex-specific fungal communities, yet we do not know whether these microbes have a differential effect on the growth and physiology of male and female genotypes. Using a common-garden design, we reared ten axenic genotypes …

Robust Microplate-Based Methods For Culturing And In Vivo Phenotypic Screening Of Chlamydomonas Reinhardtii, Timothy C. Haire, Cody Bell, Kirstin Cutshaw, Brendan Swiger, Kurt Winkelmann, Andrew G. Palmer

Biomedical Engineering and Sciences Faculty Publications

Chlamydomonas reinhardtii (Cr), a unicellular alga, is routinely utilized to study photosynthetic biochemistry, ciliary motility, and cellular reproduction. Its minimal culture requirements, unicellular morphology, and ease of transformation have made it a popular model system. Despite its relatively slow doubling time, compared with many bacteria, it is an ideal eukaryotic system for microplate-based studies utilizing either, or both, absorbance as well as fluorescence assays. Such microplate assays are powerful tools for researchers in the areas of toxicology, pharmacology, chemical genetics, biotechnology, and more. However, while microplate-based assays are valuable tools for screening biological systems, these methodologies can significantly alter the …

Comparative Meiotic Cytology Among Drosophila Species, Ahmed Folademi Majekodunmi

College of Science and Health Theses and Dissertations

Physical connections established by homologous recombination are normally sufficient to establish proper co-orientation of chromosomes during prometaphase of female meiosis I. Nonexchange chromosomes can still segregate because they are connected by heterochromatic threads, which are thought to connect homologous chromosomes and ensure co-orientation in the absence of a chiasma. In Drosophila, the nonexchange chromosomes (such as the Muller F element, also called the “dot chromosome,” which never undergoes recombination) move out on the spindle during prometaphase I, and can be found positioned between the spindle poles and the exchange chromosomes at the metaphase plate. By metaphase I arrest, these …

Ecosystem Function And Phenotypic Variation In Spartina Alterniflora Salt Marshes, Sandra E. Voors

USF Tampa Graduate Theses and Dissertations

Biodiversity is important to ecosystem function at many scales, and variation functional traits within a species can potentially influence ecosystem functioning by altering nutrient cycling dynamics. High population extinction rates are resulting in a rapid loss of within-species biodiversity, so there is a need to better understand the importance of intraspecific variation to ecosystem-level processes. Tidal salt marshes are ideal ecosystems for investigating intraspecific variation in plant-nutrient relationships because they are dominated by a monoculture of the foundation species Spartina alterniflora, with distinct phenotypes that correspond to environmental gradients across the marsh. We conducted a field survey of existing …

Killi-Data News (Fall), Tyrone Genade

Killifish Research Review

Many interesting papers have been published over the last three months. The large volume of papers coupled with the start of the new college semester (and the workload it brings) delayed this issue of Killi-Data News. But better late than never—or so I hope! In this issue Richard van der Laan provides an insightful review of the recent Aphanius papers as to their taxonomic implications and questions. The systematic issues he raises show the importance of the Molecular project: we need to get more samples of the various cyprinodontiforme families to resolve unsettled systematic and taxonomic issues. In the Next …

Factors Affecting The Parasitism Of Gregarine Species In Grasshoppers In Western Nebraska, Alexandra Creigh, Kristin Mclarty, Scott Lyell Gardner

Honors Program: Senior Projects (Public)

We conducted a survey of the species of parasites found in grasshoppers around the area of Dunwoody’s Pond to investigate whether there were any species specific parasitic relationships occurring there. We collected grasshoppers from several areas around Dunwoody’s Pond totaling 15 species including Melanoplus bivittatus (Say 1825) , Melanoplus sanguinipes (Fabricius, 1798) , Melanoplus differentialis (Thomas 1865), and Melanoplus femurrubrum (De Geer 1773), along with others (Seymour et al., 2009) and compared the parasites found in them. This study is similar to one conducted in South America by Lloyd in 1951, and we hoped to find connections between species to …

Flames And Frogs – The Impact Of Environmental Disturbances On Host-Parasite Dynamics, Nicole Ortega

USF Tampa Graduate Theses and Dissertations

The successful completion of this work is dedicated first to my grandparents for having always shown their unwavering love and encouragement in my journeys (most of which they kindly and politely only pretended to understand) and for having also served as life-long role models who upheld an unparalleled work ethic. To many whom I consider to be my chosen family, especially Ann Williams and Brittany Sears, who kept me laughing, but more importantly, kept my crazy train from derailing during these tumultuous years. To Wayne Price and Tom Jackman, who fostered the success of my career and are the epitome …

Studies Of Amino Acid Mutations In Drug Resistance Of The Smo Protein, Eunice Wintona

UNO Student Research and Creative Activity Fair

Smoothened receptor (SMO) is a protein that in humans, is encoded by the SMO gene. A systemic mutation in its binding pocket helps predict the sensitivity of mutant proteins to different drugs. Known as a GPCR-like receptor, it is a component of the hedgehog signaling pathway; a pathway involved in body patterning and the regulation of adult stem cells. An uncontrolled or inappropriate activation of the Hedgehog pathway drives tumor progression in cancers and a number of birth defects. To achieve these goals, the molecular modeling software MOE was used to build small molecules and drug molecules like Vismodegib and …

Genetic Diversity And Distinctness Of Wild Nebraska Hops And Hop Cultivars (Humulus Lupulus L.), Megan Franklin

Honors Program: Senior Projects (Public)

Background Commercial hop (Humulus lupulus) cultivars that are being grown in the Midwest are not performing as successfully as when they are grown in the Pacific Northwest, the region to which they are adapted. To increase adaptation to the Midwest environment, one strategy is to draw from the genetic pool of wild native Midwest hops, which have developed genes that allow them to grow successfully in this environment. Wild hop plants that are genetically distinct from commercial cultivars are likely to have more adaptations, such as pest/disease resistance and drought tolerance, which can be bred into commercial lines. The …

Combinations Of Plant Water-Stress And Neonicotinoids Can Lead To Secondary Outbreaks Of Banks Grass Mite (Oligonychus Pratensis Banks), Alice Ruckert, L. Niel Allen, Ricardo A. Ramirez

Civil and Environmental Engineering Faculty Publications

Spider mites, a cosmopolitan pest of agricultural and landscape plants, thrive under hot and dry conditions, which could become more frequent and extreme due to climate change. Recent work has shown that neonicotinoids, a widely used class of systemic insecticides that have come under scrutiny for non-target effects, can elevate spider mite populations. Both water-stress and neonicotinoids independently alter plant resistance against herbivores. Yet, the interaction between these two factors on spider mites is unclear, particularly for Banks grass mite (Oligonychus pratensis; BGM). We conducted a field study to examine the effects of water-stress (optimal irrigation = 100% …

Market Integration Predicts Human Gut Microbiome Attributes Across A Gradient Of Economic Development, Keaton Stagaman, Tara J. Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan

Publications and Research

Economic development is marked by dramatic increases in the incidence of microbiome-associated diseases, such as autoimmune diseases and metabolic syndromes, but the lifestyle changes that drive alterations in the human microbiome are not known. We measured market integration as a proxy for economically related lifestyle attributes, such as ownership of specific market goods that index degree of market integration and components of traditional and nontraditional (more modern) house structure and infrastructure, and profiled the fecal microbiomes of 213 participants from a contiguous, indigenous Ecuadorian population. Despite relatively modest differences in lifestyle across the population, greater economic development correlated with significantly …

Learning And Behavior In Hatchling Trachemys Scripta Exposed To Bisphenol-A During Embryonic Development, Justin E. Dillard

Theses and Dissertations

Steroids play an integral role in orchestrating embryonic development, and can affect a suite of phenotypic traits, including learning and memory. Endocrine disrupting compounds (EDCs) can mimic the effects of steroids and can affect the same suites of phenotypic traits during embryonic development. Bisphenol-A (BPA) is an EDC that mimics the action of estrogen, and recent work is beginning to implicate BPA in effects on learning and behavior similar to those caused by estrogen treatment studies. Red-eared slider turtles (Trachemys scripta) are a good system to investigate the effects of BPA on learning and behavior, both because the molecular underpinnings …

Effect Of The Specific Carbohydrate Diet On The Microbiome Of A Primary Sclerosing Cholangitis And Ulcerative Colitis Patient, Alanna Dubrovsky, Christopher Kitts

Biological Sciences

A 20-year-old female was diagnosed with ulcerative colitis (UC) at age 14 and primary sclerosing cholangitis (PSC) at age 16. The PSC was successfully treated with high doses of oral vancomycin; however, the UC was more difficult to manage. After many drug treatments failed to treat the UC, the patient began following the specific carbohydrate diet (SCD). This report documents fecal microbiome changes resulting from following the SCD for two weeks. The DNA extracted from fecal samples was subjected to 16S rRNA gene sequencing to quantify bacterial species abundance. Not only were substantial changes in the fecal bacterial composition detectable …

Fatty Acid And Associated Gene Expression Analyses Of Three Tree Peony Species Reveal Key Genes For Α-Linolenic Acid Synthesis In Seeds, Qing-Yu Zhang, Rui Yu, Li-Hang Xie, Mahbubur Rahman, Aruna Kilaru, Li-Xin Niu, Yan-Long Zhang

ETSU Faculty Works

The increasing demand for healthy edible oil has generated the need to identify promising oil crops. Tree peony (Paeonia section Moutan DC.) is a woody oil crop with α-linolenic acid contributing for 45% of the total fatty acid (FA) content in seeds. Molecular and genetic differences that contribute to varied FA content and composition among the wild peony species are however, poorly understood. Analyses of FA content and composition during seed development in three tree peony species (P. rockii, P. potaninii, and P. lutea) showed varied FA content in the three species with highest in P. rockii, followed by P. …

Maternal Egg Hormones In The Mating Context: The Effect Of Pair Personality, S. Ruuskanen, T. G. G. Groothuis, Alexander T. Baugh, S. V. Schaper, B. De Vries, K. Van Oers

Biology Faculty Works

1. Animal personality traits emerge developmentally from the interaction of genetic and early environmental factors. Maternal hormones, such as androgens (testosterone, T and androstenedione, A4), transferred to embryos and egg yolks may simultaneously organize multiple behavioural and physiological traits. Although previous studies demonstrated an association between the mother's personality and yolk androgen levels, the independent effects of the male partner's personality and pair combination remains unknown. 2. We test this association using an ecological model species for personality research, the great tit (Parus major) using multiple approaches: (1) a wild population, (2) a randomly mated captive population and (3) an …

Condition-Dependence Of Blue Plumage Coverage In Indigo Buntings Passerina Cyanea, Spencer B. Hudson, Travis E. Wilcoxen

Biology Faculty Publications

Nuptial plumage colouration is seemingly favoured by females of avian species with regards to sexual selection. This particular secondary sexual characteristic has been previously shown to be a condition-dependent signal of individual quality among passerines with pigment-based colouration (i.e. yellows and reds). In contrast, relationships between structural plumage colouration (i.e. blues) and aspects of both physical quality and physiological function have been understudied. Using free-living Indigo Buntings (Passerina cyanea) as a study species, we compared the percentage of blue feather coverage to body condition, innate immune responses, antioxidant capacity, stress physiology, reproductive physiology, and …